Long story short: 100,000 Mixtecs lived there when the Spanish showed up in in the early 1500's. The Dominicans decided to build a church and to convert everyone to Catholicism. They designed the village surrounding the church and built an aqueduct. A good plan. Unfortunately, they also brought diseases that effectively wiped out the population with fifty years with a 95 percent kill rate. No need for a large church after that, but construction continued through the centuries and it survived various battles during the revolutions. The restoration has been ongoing for several years now as the government pushes the Ruta Domincana.
I remember the first time we went there when work on the interior of the church had barely begun. There were birds living in the huge dust filled space. It was dark and dirty and magical. Now, it is bright and white and I think it has lost a little of its magic, because so much of the patina is gone and the floors and walls are too perfect. However, the before, during and after shots are pretty dramatic.